Volume 20, Issue 8, Pages 1310-1320 (August 2012) Structure of AAV-DJ, a Retargeted Gene Therapy Vector: Cryo-Electron Microscopy at 4.5 Å Resolution  Thomas F. Lerch, Jason K. O'Donnell, Nancy L. Meyer, Qing Xie, Kenneth A. Taylor, Scott M. Stagg, Michael S. Chapman  Structure  Volume 20, Issue 8, Pages 1310-1320 (August 2012) DOI: 10.1016/j.str.2012.05.004 Copyright © 2012 Elsevier Ltd Terms and Conditions

Structure 2012 20, 1310-1320DOI: (10.1016/j.str.2012.05.004) Copyright © 2012 Elsevier Ltd Terms and Conditions

Figure 1 Representative Coulomb Potential Density from the 3D Cryo-EM Reconstruction at 4.5 Å Resolution, Compared to Corresponding Regions of the 3.0 Å Crystallographic Electron Density of AAV-2, Truncated at the Same Resolution The crystallographic map has been calculated with model-independent phases obtained through extension / refinement using 60-fold noncrystallographic symmetry (Xie et al., 2003). (A and B) Part of the clearly traceable β-barrel (A) and representative aromatic side chains (B) fit to the maps of AAV-DJ (left) and AAV-2 (right). Maps are contoured at 1.7–1.2 σ to cover comparable volumes. (C) The weakest density for the entire AAV-DJ structure is a loop containing residues 453–458. Strong, but discontinuous, density is observed at a contour of 1 σ (left), but the loop is fully traceable at a lower contour (right). See also Figure S1. Structure 2012 20, 1310-1320DOI: (10.1016/j.str.2012.05.004) Copyright © 2012 Elsevier Ltd Terms and Conditions

Figure 2 The AAV-DJ Heparin Binding Region (A) Surface electrostatic potential of AAV-DJ (left) compared to AAV-2 (right). The molecular surface of the capsid spikes is colored from positive (blue) to negative (red), viewed down the 3-fold symmetry axis (triangle). The AAV-2 heparin-binding footprint (O'Donnell et al., 2009) is outlined with HBD residues Arg585/Arg588 (AAV-2) or Arg587/Arg590 (AAV-DJ) forming the most positively charged part. The electrostatic potentials are similar with only subtle differences. Positive potential extends further above the HBD in AAV-DJ (arrows). However, the immediate vicinity of the 3-fold (triangle) is slightly positively charged in AAV-2 near where a heparin polymer would bridge between HBDs and where AAV-3B's Arg594 participates in binding (Lerch and Chapman, 2012). (B) Heparin affinity chromatography reveals that AAV-DJ binds with slightly weaker affinity than AAV-2, although it seems unlikely that the subtle differences in surface charge and heparin affinity fully explain the phenotype of AAV-DJ. VLPs were eluted in PBS supplemented with the NaCl concentrations shown, denatured, and detected by dot blot as described in the Experimental Procedures. Structure 2012 20, 1310-1320DOI: (10.1016/j.str.2012.05.004) Copyright © 2012 Elsevier Ltd Terms and Conditions

Figure 3 A Unique Loop Structure in AAV-DJ (A) Local sequence alignment for the loop, where the AAV-DJ structure is most distinct. The parental strains AAV-2, AAV-8, and AAV-9 are in bold font where their sequences are identical to AAV-DJ. (B) The distinct 3D structure for this loop is highlighted with this stereographic pair showing the AAV-DJ structure (colored by atom type) superimposed on the EM density. For comparison, the backbones of parental serotypes of known structure are shown, AAV-2 (red) and AAV-8 (blue). (C) Alignment of all known AAV structures further demonstrates the unique conformation of AAV-DJ at VR-I. AAV-1 (pink; PDB ID 3NG9), AAV-2 (red) (Xie et al., 2002), AAV-3B (orange) (Lerch et al., 2010), AAV-4 (yellow) (Govindasamy et al., 2006), AAV-5 (wheat; PDB ID 3NTT), AAV-6 (violet) (Xie et al., 2011), and AAV-8 (blue) (Nam et al., 2007). Structure 2012 20, 1310-1320DOI: (10.1016/j.str.2012.05.004) Copyright © 2012 Elsevier Ltd Terms and Conditions

Figure 4 Distinctive Structural Features of AAV-DJ Are Concentrated in a Dominant Antigenic Site (A) A surface projection, calculated by RIVEM (Xiao and Rossmann, 2007), is colored by distance from the viral center (blue to red). The triangular area is 1 of 60 icosahedral equivalents covering the capsid surface and is bounded by a 5-fold axis (pentagon) and 3-folds (triangle). The VR-I loop (dashed black outline) is displaced ∼4 Å relative to AAV-2 because of a Ser-Gly insertion (solid black outline), disrupting the footprint of the AAV-2 binding site (yellow outline) of neutralizing mouse monoclonal antibody A20 (Lochrie et al., 2006; Wobus et al., 2000), as visualized by cryo-EM (McCraw et al., 2012). (B) A stereographic pair in which the VR-1 structure of AAV-DJ (green) is superimposed on the crystal structure of AAV-2 (red) and the envelope of a bound FAb' fragment from mAb A20. The arrow points to a steric conflict that explains the lack of A20 binding to AAV-DJ. (C) AAV-DJ VLPs do not bind to purified A20 in a native dot-blot, whereas AAV-2 is readily detected. (D and E) Surface projections showing where the amino acid sequence of AAV-DJ differs from AAV-2 (D) and where the Cα differences are greater than 1.5 Å (E). The experimentally visualized mAb A20 (purple) and heparin (red) footprints from AAV-2 are superimposed. (D and E) Emphasize that AAV-DJ is more unique within the epitope than the primary receptor binding site. Structure 2012 20, 1310-1320DOI: (10.1016/j.str.2012.05.004) Copyright © 2012 Elsevier Ltd Terms and Conditions